Estimates diversity of a metacommunity.
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q |
A number: the order of diversity. |
MC |
A |
Biased |
Logical; if |
Correction |
A string containing one of the possible corrections. The correction must be accepted by |
Tree |
An object of class |
Normalize |
If |
Z |
A relatedness matrix, i.e. a square matrix whose terms are all positive, strictly positive on the diagonal. Generally, the matrix is a similarity matrix, i.e. the diagonal terms equal 1 and other terms are between 0 and 1. |
Simulations |
The number of simulations to build confidence intervals. |
CheckArguments |
Logical; if |
x |
An object to be tested or plotted. |
main |
The title of the plot. |
Which |
May be |
object |
A |
... |
Additional arguments to be passed to the generic methods. |
Divest
estimates the diversity of the metacommunity and partitions it into alpha and beta components.
If Tree
is provided, the phylogenetic diversity is calculated else if Z
is not NULL
, then similarity-based entropy is calculated.
Bootstrap confidence intervals are calculated by drawing simulated communities from a multinomial distribution following the observed frequencies (Marcon et al, 2012; 2014).
A Divest
object which is a DivPart
object with an additional item in its list:
SimulatedDiversity |
A matrix containing the simulated values of alpha, beta and gamma diversity. |
Divest
objects can be summarized and plotted.
Eric Marcon <Eric.Marcon@ecofog.gf> and Bruno Herault <Bruno.Herault@ecofog.gf>
Marcon, E., Herault, B., Baraloto, C. and Lang, G. (2012). The Decomposition of Shannon's Entropy and a Confidence Interval for Beta Diversity. Oikos 121(4): 516-522.
Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. PLOS One 9(3): e90289.
Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. Methods in Ecology and Evolution 6(3): 333-339.
DivPart
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Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
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